Glenys Stacey, the head of Ofqual, suggested that proposals to abolish foundation and higher tier papers – requiring all pupils to sit the same test – could undermine the “universal” nature of examinations.

The comments threaten to undermine a key element of the Government’s wide-ranging plan to overhaul the examinations system in England.

Currently, GCSEs are split into two levels. Foundation papers are traditionally aimed at low-ability pupils, allowing them to score a maximum C grade in tests.

But Michael Gove, the Education Secretary, has condemned the move for promoting a "culture of low expectations".

He said the system made it impossible for thousands of students to achieve the decent grades needed to get good jobs and proceed onto A-level courses.

Under a shake-up of GCSEs, he wants to axe tiered papers and force all pupils to sit the same exam.

But giving evidence to the Commons Education Select Committee today, Ms Stacey appeared to suggest that Ofqual may refuse to endorse the move, forcing the Government to drop the proposal.

She said Ofqual must “have regard to Government policy but not to slavishly follow it”.

"It is Ofqual's job to determine whether or not new GCSEs will be tiered or whether there is a better arrangement that could ensure that these qualifications remain universal, as the Secretary of State has asked, and remain accessible to the same proportion of students as they are now," she said.

Ms Stacey said there were pros and cons of running tiered exams.

She added: "The important point here is that we know that's our job and we will make the right decision about what is the best known way to ensure that these qualifications remain universal and accessible.

“It may be tiering, it may not, but we have a job to do to get to the right solution."

The comments were made as part of an evidence session on last year’s English GCSE grading fiasco.

Exam boards suddenly shifted grade boundaries up between tests taken in January and June – resulting in tens of thousands of pupils missing out on good grades.

Ms Stacey said major changes to GCSEs – including the abolition of bite-sized modular courses – would probably off-set a repeat of the episode this year.

But she insisted there would still be "variations" between results in different schools. "We cannot guarantee that there will be no variations between schools,” she said. “That's what you would expect."